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[ENH] add min/max len #35

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Merged
36000 merged 2 commits into from
Feb 25, 2026
Merged

[ENH] add min/max len #35

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de1e7c6
[ENH] add min/max len
36000 Feb 25, 2026
682ed06
better handling of buffer sizes
36000 Feb 25, 2026
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11 changes: 8 additions & 3 deletions cuslines/cuda_python/cu_propagate_seeds.py
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Original file line number Diff line number Diff line change
Expand Up @@ -243,7 +243,7 @@ def get_buffer_size(self):
buffer_size += lens[jj] * 3 * REAL_SIZE
return math.ceil(buffer_size / MEGABYTE)

def as_generator(self):
def as_generator(self, minlen=0, maxlen=np.inf):
def _yield_slines():
for ii in range(self.ngpus):
this_sls = self.slines[ii]
Expand All @@ -252,9 +252,14 @@ def _yield_slines():
for jj in range(self.nSlines[ii]):
npts = this_len[jj]

if npts < minlen or npts > maxlen:
continue

yield np.asarray(this_sls[jj], dtype=REAL_DTYPE)[:npts]

return _yield_slines()

def as_array_sequence(self):
return ArraySequence(self.as_generator(), self.get_buffer_size())
def as_array_sequence(self, minlen=0, maxlen=np.inf):
return ArraySequence(
self.as_generator(minlen=minlen, maxlen=maxlen),
self.get_buffer_size())
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14 changes: 8 additions & 6 deletions cuslines/cuda_python/cu_tractography.py
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Original file line number Diff line number Diff line change
Expand Up @@ -74,7 +74,7 @@ def __init__(
Maximum angle (in radians) between steps
default: radians(60)
step_size : float, optional
Step size for tracking
Step size for tracking, in voxels
default: 0.5
relative_peak_thresh : float, optional
Relative peak threshold for direction selection
Expand Down Expand Up @@ -235,7 +235,7 @@ def _divide_chunks(self, seeds):
nchunks = (seeds.shape[0] + global_chunk_sz - 1) // global_chunk_sz
return global_chunk_sz, nchunks

def generate_sft(self, seeds, ref_img):
def generate_sft(self, seeds, ref_img, minlen=0, maxlen=np.inf):
global_chunk_sz, nchunks = self._divide_chunks(seeds)
buffer_size = 0
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generators = []
Expand All @@ -246,7 +246,8 @@ def generate_sft(self, seeds, ref_img):
seeds[idx * global_chunk_sz : (idx + 1) * global_chunk_sz]
)
buffer_size += self.seed_propagator.get_buffer_size()
generators.append(self.seed_propagator.as_generator())
generators.append(self.seed_propagator.as_generator(
minlen=minlen, maxlen=maxlen))
pbar.update(
seeds[idx * global_chunk_sz : (idx + 1) * global_chunk_sz].shape[0]
)
Expand All @@ -255,12 +256,12 @@ def generate_sft(self, seeds, ref_img):
)
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return StatefulTractogram(array_sequence, ref_img, Space.VOX)

def generate_trx(self, seeds, ref_img):
def generate_trx(self, seeds, ref_img, minlen=0, maxlen=np.inf):
global_chunk_sz, nchunks = self._divide_chunks(seeds)

# Will resize by a factor of 2 if these are exceeded
sl_len_guess = 100
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Copilot AI Feb 25, 2026

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The change from sl_per_seed_guess = 4 to sl_per_seed_guess = 2 appears unrelated to adding min/max length filtering. This change affects memory allocation for TRX file generation and could impact performance if the actual number of streamlines per seed exceeds this guess (causing more frequent resizes). If this change is intentional and related to the filtering reducing expected streamlines per seed, it should be documented in the PR description or as a comment in the code.

Suggested change
sl_len_guess = 100
sl_len_guess = 100
# Heuristic: initial guess of how many streamlines we get per seed.
# With the current min/max length filtering in the GPU propagator we
# typically obtain fewer valid streamlines per seed than before, so
# we lower the guess from 4 to 2 to avoid over-allocating memory.
# If the filtering or seeding strategy changes (e.g. more accepted
# streamlines per seed), this value should be re-evaluated to balance
# memory usage against the cost of TRX internal resizes.

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sl_per_seed_guess = 4
sl_per_seed_guess = 2
n_sls_guess = sl_per_seed_guess * seeds.shape[0]

# trx files use memory mapping
Expand All @@ -284,7 +285,8 @@ def generate_trx(self, seeds, ref_img):
seeds[idx * global_chunk_sz : (idx + 1) * global_chunk_sz]
)
tractogram = Tractogram(
self.seed_propagator.as_array_sequence(),
self.seed_propagator.as_array_sequence(
minlen=minlen, maxlen=maxlen),
affine_to_rasmm=ref_img.affine,
)
tractogram.to_world()
Expand Down
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